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Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions. Proc Natl Acad Sci U S A 2019; 116:23075-23082. [PMID: 31666318 DOI: 10.1073/pnas.1913418116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
RNA folding is often studied by renaturing full-length RNA in vitro and tracking folding transitions. However, the intracellular transcript folds as it emerges from the RNA polymerase. Here, we investigate the folding pathways and stability of numerous late-transcriptional intermediates of yeast and Escherichia coli transfer RNAs (tRNAs). Transfer RNA is a highly regulated functional RNA that undergoes multiple steps of posttranscriptional processing and is found in very different lengths during its lifetime in the cell. The precursor transcript is extended on both the 5' and 3' ends of the cloverleaf core, and these extensions get trimmed before addition of the 3'-CCA and aminoacylation. We studied the thermodynamics and structures of the precursor tRNA and of late-transcriptional intermediates of the cloverleaf structure. We examined RNA folding at both the secondary and tertiary structural levels using multiple biochemical and biophysical approaches. Our findings suggest that perhaps nature has selected for a single-base addition to control folding to the functional 3D structure. In near-cellular conditions, yeast tRNAPhe and E. coli tRNAAla transcripts fold in a single, cooperative transition only when nearly all of the nucleotides in the cloverleaf are transcribed by indirectly enhancing folding cooperativity. Furthermore, native extensions on the 5' and 3' ends do not interfere with cooperative core folding. This highly controlled cooperative folding has implications for recognition of tRNA by processing and modification enzymes and quality control of tRNA in cells.
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Ong AAL, Toh DFK, Patil KM, Meng Z, Yuan Z, Krishna MS, Devi G, Haruehanroengra P, Lu Y, Xia K, Okamura K, Sheng J, Chen G. General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase. Biochemistry 2019; 58:1319-1331. [PMID: 30775913 DOI: 10.1021/acs.biochem.8b01313] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA·RNA-RNA triplex formation. Triplex formation is favored for RNA duplexes with a purine tract within one of the RNA duplex strands, and is severely destabilized if the purine tract is interrupted by pyrimidine residues. Here, we report the synthesis of a PNA monomer incorporated with an artificial nucleobase S, followed by the binding studies of a series of S-modified PNAs. Our data suggest that an S residue incorporated into short 8-mer dsRNA-binding PNAs (dbPNAs) can recognize internal Watson-Crick C-G and U-A, and wobble U-G base pairs (but not G-C, A-U, and G-U pairs) in RNA duplexes. The short S-modified PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. Interestingly, replacement of the C residue in an S·C-G triple with a 5-methyl C results in the disruption of the triplex, probably due to a steric clash between S and 5-methyl C. Previously reported PNA E base shows recognition of U-A and A-U pairs, but not a U-G pair. Thus, S-modified dbPNAs may be uniquely useful for the general recognition of RNA U-G, U-A, and C-G pairs. Shortening the succinyl linker of our PNA S monomer by one carbon atom to have a malonyl linker causes a severe destabilization of triplex formation. Our experimental and modeling data indicate that part of the succinyl moiety in a PNA S monomer may serve to expand the S base forming stacking interactions with adjacent PNA bases.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhenyu Meng
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhen Yuan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore , Singapore , 117604.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore , 639798
| | - Jia Sheng
- Department of Chemistry and The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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Leamy KA, Yennawar NH, Bevilacqua PC. Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms. Biochemistry 2018; 57:2994-3002. [PMID: 29733204 PMCID: PMC6726375 DOI: 10.1021/acs.biochem.8b00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A diverse set of organisms has adapted to live under extreme conditions. The molecular origin of the stability is unclear, however. It is not known whether the adaptation of functional RNAs, which have intricate tertiary structures, arises from strengthening of tertiary or secondary structure. Herein we evaluate effects of sequence changes on the thermostability of tRNAphe using experimental and computational approaches. To separate out effects of secondary and tertiary structure on thermostability, we modify base pairing strength in the acceptor stem, which does not participate in tertiary structure. In dilute solution conditions, strengthening secondary structure leads to non-two-state thermal denaturation curves and has small effects on thermostability, or the temperature at which tertiary structure and function are lost. In contrast, under cellular conditions with crowding and Mg2+-chelated amino acids, where two-state cooperative unfolding is maintained, strengthening secondary structure enhances thermostability. Investigation of stabilities of each tRNA stem across 44 organisms with a range of optimal growing temperatures revealed that organisms that grow in warmer environments have more stable stems. We also used Shannon entropies to identify positions of higher and lower information content, or sequence conservation, in tRNAphe and found that secondary structures have modest information content allowing them to drive thermal adaptation, while tertiary structures have maximal information content hindering them from participating in thermal adaptation. Base-paired regions with no tertiary structure and modest information content thus offer a facile evolutionary route to enhancing the thermostability of functional RNA by the simple molecular rules of base pairing.
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Affiliation(s)
- Kathleen A Leamy
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Neela H Yennawar
- Huck Institutes of the Life Sciences , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Philip C Bevilacqua
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biochemistry and Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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Strulson CA, Boyer JA, Whitman EE, Bevilacqua PC. Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA (NEW YORK, N.Y.) 2014; 20:331-47. [PMID: 24442612 PMCID: PMC3923128 DOI: 10.1261/rna.042747.113] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 11/22/2013] [Indexed: 05/21/2023]
Abstract
Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg(2+) ion concentrations are low, K(+) concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg(2+) (0.5-2 mM) and K(+) (140 mM) if the solution is supplemented with physiological amounts (∼ 20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperature-dependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.
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Affiliation(s)
- Christopher A. Strulson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Joshua A. Boyer
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elisabeth E. Whitman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C. Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Corresponding authorE-mail
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Zhou Y, Kierzek E, Loo ZP, Antonio M, Yau YH, Chuah YW, Geifman-Shochat S, Kierzek R, Chen G. Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides. Nucleic Acids Res 2013; 41:6664-73. [PMID: 23658228 PMCID: PMC3711454 DOI: 10.1093/nar/gkt352] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Triplex is emerging as an important RNA tertiary structure motif, in which consecutive non-canonical base pairs form between a duplex and a third strand. RNA duplex region is also often functionally important site for protein binding. Thus, triplex-forming oligonucleotides (TFOs) may be developed to regulate various biological functions involving RNA, such as viral ribosomal frameshifting and reverse transcription. How chemical modification in TFOs affects RNA triplex stability, however, is not well understood. Here, we incorporated locked nucleic acid, 2-thio U- and 2′-O methyl-modified residues in a series of all pyrimidine RNA TFOs, and we studied the binding to two RNA hairpin structures. The 12-base-triple major-groove pyrimidine–purine–pyrimidine triplex structures form between the duplex regions of RNA/DNA hairpins and the complementary RNA TFOs. Ultraviolet-absorbance-detected thermal melting studies reveal that the locked nucleic acid and 2-thio U modifications in TFOs strongly enhance triplex formation with both parental RNA and DNA duplex regions. In addition, we found that incorporation of 2′-O methyl-modified residues in a TFO destabilizes and stabilizes triplex formation with RNA and DNA duplex regions, respectively. The (de)stabilization of RNA triplex formation may be facilitated through modulation of van der Waals contact, base stacking, hydrogen bonding, backbone pre-organization, geometric compatibility and/or dehydration energy. Better understanding of the molecular determinants of RNA triplex structure stability lays the foundation for designing and discovering novel sequence-specific duplex-binding ligands as diagnostic and therapeutic agents targeting RNA.
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Affiliation(s)
- Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore
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Wan Y, Russell R. Enhanced specificity against misfolding in a thermostable mutant of the Tetrahymena ribozyme. Biochemistry 2011; 50:864-74. [PMID: 21174447 DOI: 10.1021/bi101467q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structured RNAs encode native conformations that are more stable than the vast ensembles of alternative conformations, but how this specificity is evolved is incompletely understood. Here we show that a variant of the Tetrahymena group I intron ribozyme that was generated previously by in vitro selection for enhanced thermostability also displays modestly enhanced specificity against a stable misfolded structure that is globally similar to the native state, despite the absence of selective pressure to increase the energy gap between these structures. The enhanced specificity for native folding arises from mutations in two nucleotides that are close together in space in the native structure, and additional experiments show that these two mutations do not affect the stability of the misfolded conformation relative to the largely unstructured transition state ensemble for interconversion between the native and misfolded conformers. Thus, they selectively stabilize the native state, presumably by strengthening a local tertiary contact network that cannot form in the misfolded conformation. The stabilization is larger in the presence of the peripheral element P5abc, suggesting that cooperative tertiary structure formation plays a key role in the enhanced stability. The increased specificity in the absence of explicit selection suggests that the large energy gap in the wild-type RNA may have arisen analogously, a consequence of selective pressure for stability of the functional structure. More generally, the structural rigidity and intricate networks of contacts in structured RNAs may allow them to evolve substantial structural specificity without explicit negative selection, even against closely related alternative structures.
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Affiliation(s)
- Yaqi Wan
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
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Finch E, Cruz C, Sloman KA, Kudoh T. Heterochrony in the germ ring closure and tail bud formation in embryonic development of rainbow trout (Oncorhynchus mykiss). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:187-95. [PMID: 19911422 DOI: 10.1002/jez.b.21325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Due to their large yolk size, salmonid embryos take a longer time for epiboly movements and germ ring closure compared with most other teleost species. Here we analyzed the germ ring closure, tail bud formation and development of the notochord and somites in rainbow trout using live embryo imaging and in situ hybridization with the rt-ntl probe. Rt-ntl is expressed in the germ ring (blastula, gastrula and somitogenesis stage), notochord, tail bud and somites (somitogenesis stage). When epiboly covers half the yolk, a tail bud-like structure is formed and somitogenesis starts. By the time epiboly is completed, the yolk covered and the germ ring closed, the embryo has already reached the 20 somite stage. Therefore, the timing of germ ring closure and tail bud formation is reversed in trout embryos compared with zebrafish and other small model fish embryos (heterochrony). Based on this result, we re-examined the definition of tail bud formation.
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Affiliation(s)
- Emma Finch
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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Nakano SI, Karimata HT, Kitagawa Y, Sugimoto N. Facilitation of RNA Enzyme Activity in the Molecular Crowding Media of Cosolutes. J Am Chem Soc 2009; 131:16881-8. [DOI: 10.1021/ja9066628] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Frontier Institute for Biomolecular Engineering Research (FIBER), and Department of Chemistry, Faculty of Science and Engineering, Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hisae Tateishi Karimata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Frontier Institute for Biomolecular Engineering Research (FIBER), and Department of Chemistry, Faculty of Science and Engineering, Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Yuichi Kitagawa
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Frontier Institute for Biomolecular Engineering Research (FIBER), and Department of Chemistry, Faculty of Science and Engineering, Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Frontier Institute for Biomolecular Engineering Research (FIBER), and Department of Chemistry, Faculty of Science and Engineering, Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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Bevilacqua PC, Blose JM. Structures, kinetics, thermodynamics, and biological functions of RNA hairpins. Annu Rev Phys Chem 2008; 59:79-103. [PMID: 17937599 DOI: 10.1146/annurev.physchem.59.032607.093743] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most RNA comprises one strand and therefore can fold back on itself to form complex structures. At the heart of these structures is the hairpin, which is composed of a stem having Watson-Crick base pairing and a loop wherein the backbone changes directionality. First, we review the structure of hairpins including diversity in the stem, loop, and closing base pair. The function of RNA hairpins in biology is discussed next, including roles for isolated hairpins, as well as hairpins in the context of complex tertiary structures. We describe the kinetics and thermodynamics of hairpin folding including models for hairpin folding, folding transition states, and the cooperativity of folding. Lastly, we discuss some ways in which hairpins can influence the folding and function of tertiary structures, both directly and indirectly. RNA hairpins provide a simple means of controlling gene expression that can be understood in the language of physical chemistry.
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Affiliation(s)
- Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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